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Tag: structure-prediction/limitations
19 items with this tag.
Apr 28, 2026
Coevolutionary patterns in multiple sequence alignments do not contribute to protein-protein complex prediction
structure-prediction/limitations
protein-protein-interactions
Apr 21, 2026
Variable regions can adopt multiple interchain orientations, and these are difficult to predict
structure-prediction/limitations
antibody-antigen-interactions/complex-prediction
Apr 21, 2026
All-atom protein structure prediction methods are unable to model PPIs with large buried surface areas
structure-prediction/limitations
structure-prediction/complex-prediction
Apr 21, 2026
Correct protomer structure prediction is necessary but insufficient for accurate protein-protein docking
structure-prediction/limitations
structure-prediction/complex-prediction
Apr 21, 2026
DL ligand docking methods generate unrealistic poses
structure-prediction/limitations
ligand-docking
Apr 21, 2026
DL structure prediction methods cannot predict CDR conformations unseen during training
cdrh3
structure-prediction/limitations
antibodies/engineering-and-design
Apr 21, 2026
DL structure tools introduce chiral errors such as swapped chiral centers, D-amino acids, and cis-amide bonds
structure-prediction/limitations
diffusion-guidance/structure-prediction
Apr 21, 2026
Protein folding neural networks can be subject to adversarial attacks
structure-prediction/limitations
alphafold2
Apr 21, 2026
Protein folding neural networks cannot predict protein stability
structure-prediction/limitations
thermostability/prediction
plddt
Apr 21, 2026
Protein folding neural networks do not extrapolate to new ligand binding sites
structure-prediction/limitations
Apr 21, 2026
Protein folding neural networks do not learn the physics of protein folding for most proteins
structure-prediction/limitations
Apr 21, 2026
Protein folding neural networks make local optimizations in the absence of coevolutionary information
structure-prediction/limitations
alphafold2
Apr 21, 2026
Protein structure prediction methods are unable to predict the energetics of a conformational landscape unless explicitly trained for that purpose
structure-prediction/limitations
conformational-dynamics/modeling
Apr 21, 2026
Protein-ligand co-folding methods do not generalize beyond their training set
ligand-docking
structure-prediction/limitations
alphafold3
Apr 21, 2026
Randomly masking residues prior to running ESMFold allows false positives to be identified more effectively
structure-prediction/limitations
thermostability/prediction
plddt
Apr 21, 2026
Unfolded and nonfunctional isoforms of folded proteins are incorrectly predicted as folded by protein folding neural networks
structure-prediction/limitations
thermostability/prediction
Apr 21, 2026
All-atom structure prediction of RNA is driven by memorization
structure-prediction/limitations
Apr 21, 2026
Crystal structures can have nonphysiological salt bridges
structure-prediction/limitations
Apr 21, 2026
Memorization in protein structure prediction
structure-prediction/limitations